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Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

Adam D Ewing1, Tracy J Ballinger1, Dent Earl1, Broad Institute Genome Sequencing and Analysis Program and Platform3, Christopher C Harris4, Li Ding4, Richard K Wilson4 and David Haussler12*

Author affiliations

1 Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA

2 Howard Hughes Medical Institute, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA

3 Broad Institute of MIT and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA

4 The Genome Institute, Washington University, 4444 Forest Park Avenue, St. Louis, MO 63108, USA

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Citation and License

Genome Biology 2013, 14:R22  doi:10.1186/gb-2013-14-3-r22

Published: 13 March 2013

Abstract

Background

Retroposed processed gene transcripts are an important source of material for new gene formation on evolutionary timescales. Most prior work on gene retrocopy discovery compared copies in reference genome assemblies to their source genes. Here, we explore gene retrocopy insertion polymorphisms (GRIPs) that are present in the germlines of individual humans, mice, and chimpanzees, and we identify novel gene retrocopy insertions in cancerous somatic tissues that are absent from patient-matched non-cancer genomes.

Results

Through analysis of whole-genome sequence data, we found evidence for 48 GRIPs in the genomes of one or more humans sequenced as part of the 1,000 Genomes Project and The Cancer Genome Atlas, but which were not in the human reference assembly. Similarly, we found evidence for 755 GRIPs at distinct locations in one or more of 17 inbred mouse strains but which were not in the mouse reference assembly, and 19 GRIPs across a cohort of 10 chimpanzee genomes, which were not in the chimpanzee reference genome assembly. Many of these insertions are new members of existing gene families whose source genes are highly and widely expressed, and the majority have detectable hallmarks of processed gene retrocopy formation. We estimate the rate of novel gene retrocopy insertions in humans and chimps at roughly one new gene retrocopy insertion for every 6,000 individuals.

Conclusions

We find that gene retrocopy polymorphisms are a widespread phenomenon, present a multi-species analysis of these events, and provide a method for their ascertainment.